Variant report

Variant	rs2066295
Chromosome Location	chr6:26168903-26168904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26168140..26172171-chr6:27111369..27115224,6	K562	blood:
2	chr6:26166351..26169370-chr6:27112939..27116064,5	K562	blood:

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1009181	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1059490	0.87[ASN][1000 genomes]
rs16891401	0.81[YRI][hapmap]
rs2183947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4486004	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72834694	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72834696	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs806973	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9366639	0.82[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs9379827	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9379828	0.87[ASN][1000 genomes]
rs9379829	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9379830	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9379831	1.00[ASW][hapmap];0.80[CEU][hapmap];0.86[CHD][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
8	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
9	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
10	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
11	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
12	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
13	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
14	nsv1025493	chr6:26026870-26223838	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1001 gene(s)	inside rSNPs	diseases
15	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
16	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
17	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
18	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases
19	nsv518431	chr6:26148311-26211368	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	521 gene(s)	inside rSNPs	diseases
20	nsv526456	chr6:26148311-26211368	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	521 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2066295	HIST1H3H	cis	parietal	SCAN
rs2066295	HIST1H4H	cis	parietal	SCAN
rs2066295	ZSCAN23	cis	cerebellum	SCAN
rs2066295	HIST1H2BJ	cis	cerebellum	SCAN
rs2066295	HIST1H1C	cis	parietal	SCAN
rs2066295	SCGN	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26159800-26171800	Weak transcription	Lung	lung
2	chr6:26160000-26171800	Weak transcription	Ovary	ovary
3	chr6:26160200-26170400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:26160200-26171600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:26160200-26171600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:26160400-26171200	Weak transcription	Osteobl	bone
7	chr6:26160400-26171400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:26160400-26171600	Weak transcription	Right Ventricle	heart
9	chr6:26160400-26171600	Weak transcription	HSMMtube	muscle
10	chr6:26160400-26171800	Weak transcription	Esophagus	oesophagus
11	chr6:26160600-26169400	Weak transcription	Fetal Kidney	kidney
12	chr6:26160600-26170200	Weak transcription	Hela-S3	cervix
13	chr6:26160600-26170400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:26160600-26170600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:26160600-26171200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:26160600-26171200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:26160600-26171200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:26160600-26171200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:26160600-26171400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:26160600-26171400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:26160600-26171400	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:26160600-26171400	Weak transcription	Psoas Muscle	Psoas
23	chr6:26160600-26171600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:26160600-26171600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:26160600-26171600	Weak transcription	Aorta	Aorta
26	chr6:26160600-26171600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:26160600-26171600	Weak transcription	Brain Substantia Nigra	brain
28	chr6:26160600-26171800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:26160800-26169000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:26160800-26171000	Weak transcription	Fetal Lung	lung
31	chr6:26160800-26171200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:26160800-26171200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:26160800-26171400	Weak transcription	Brain Anterior Caudate	brain
34	chr6:26160800-26171600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:26160800-26171600	Weak transcription	Colonic Mucosa	Colon
36	chr6:26161200-26169800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:26161800-26170000	Weak transcription	A549	lung
38	chr6:26162600-26171600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:26163000-26170400	Weak transcription	Small Intestine	intestine
40	chr6:26164400-26169400	Weak transcription	GM12878-XiMat	blood
41	chr6:26164600-26170200	Weak transcription	Primary T cells from cord blood	blood
42	chr6:26164600-26171000	Weak transcription	Stomach Mucosa	stomach
43	chr6:26164600-26171400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr6:26164600-26171600	Weak transcription	Brain Hippocampus Middle	brain
45	chr6:26164600-26171600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:26164600-26171800	Weak transcription	Left Ventricle	heart
47	chr6:26164600-26172000	Weak transcription	Gastric	stomach
48	chr6:26164800-26171200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:26164800-26171200	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:26164800-26171400	Weak transcription	Rectal Mucosa Donor 31	rectum

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